{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T00:09:39Z","timestamp":1747181379523,"version":"3.40.5"},"reference-count":52,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T00:00:00Z","timestamp":1681257600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,12]]},"abstract":"<jats:p>While the world is still recovering from the Covid-19 pandemic, monkeypox virus (MPXV) awaits to cause another global outbreak as a challenge to all of mankind. However, the Covid-19 pandemic has taught us a lesson to speed up the pace of viral genomic research for the implementation of preventive and treatment strategies. One of the important aspects of MPXV that needs immediate insight is its evolutionary lineage based on genomic studies. Utilizing high-quality isolates from the GISAID (Global Initiative on Sharing All Influenza Data) database, primarily sourced from Europe and North America, we employed a SNP-based whole-genome phylogeny method and identified four major clusters among 628 MPXV isolates. Our findings indicate a distinct evolutionary lineage for the first MPXV isolate, and a complex epidemiology and evolution of MPXV strains across various countries. Further analysis of the host\u2013pathogen interaction network revealed key viral proteins, such as E3, SPI-2, K7 and CrmB, that play a significant role in regulating the network and inhibiting the host\u2019s cellular innate immune system. Our structural analysis of proteins E3 and CrmB revealed potential disruption of stability due to certain mutations. While this study identified a large number of mutations within the new outbreak clade, it also reflected that we need to move fast with the genomic analysis of newly detected strains from around the world to develop better prevention and treatment methods.<\/jats:p>","DOI":"10.1099\/mgen.0.000987","type":"journal-article","created":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T16:35:34Z","timestamp":1681317334000},"source":"Crossref","is-referenced-by-count":9,"title":["Monkeypox virus: phylogenomics, host\u2013pathogen interactome and mutational cascade"],"prefix":"10.1099","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4942-4459","authenticated-orcid":false,"given":"Roshan","family":"Kumar","sequence":"first","affiliation":[{"name":"Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar 824234, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shekhar","family":"Nagar","sequence":"additional","affiliation":[{"name":"Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shazia","family":"Haider","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Jaypee Institute of Information and Technology, Uttar Pradesh, Noida 201309, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Utkarsh","family":"Sood","sequence":"additional","affiliation":[{"name":"Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kalaiarasan","family":"Ponnusamy","sequence":"additional","affiliation":[{"name":"Biotechnology and Viral Hepatitis Division, National Centre for Disease Control, New Delhi 110054, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gauri Garg","family":"Dhingra","sequence":"additional","affiliation":[{"name":"Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shailly","family":"Anand","sequence":"additional","affiliation":[{"name":"Deen Dayal Upadhyaya College, University of Delhi, New Delhi 110078, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ankita","family":"Dua","sequence":"additional","affiliation":[{"name":"Shivaji College, University of Delhi, New Delhi 110027, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mona","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roushan","family":"Kumar","sequence":"additional","affiliation":[{"name":"Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar 824234, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manisha","family":"Sengar","sequence":"additional","affiliation":[{"name":"Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Indrakant Kumar","family":"Singh","sequence":"additional","affiliation":[{"name":"Institute of Eminence, Delhi School of Public Health, University of Delhi, Delhi 110007, India"},{"name":"Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rup","family":"Lal","sequence":"additional","affiliation":[{"name":"Phixgen Pvt. Ltd., Sector 55, Noida, Uttar Pradesh, India"},{"name":"Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","first-page":"593","article-title":"A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo","volume":"46","author":"Ladnyj","year":"1972","journal-title":"Bull World Health Organ"},{"doi-asserted-by":"publisher","key":"R2","DOI":"10.3389\/fpubh.2018.00241"},{"doi-asserted-by":"publisher","key":"R3","DOI":"10.1111\/1751-7915.14224"},{"doi-asserted-by":"publisher","key":"R4","DOI":"10.3390\/v14102134"},{"doi-asserted-by":"publisher","key":"R5","DOI":"10.1128\/mBio.01495-21"},{"doi-asserted-by":"publisher","key":"R6","DOI":"10.3201\/eid2604.191164"},{"doi-asserted-by":"publisher","key":"R7","DOI":"10.1016\/S1473-3099(22)00228-6"},{"doi-asserted-by":"publisher","key":"R8","DOI":"10.1128\/mSystems.00505-20"},{"doi-asserted-by":"publisher","key":"R9","DOI":"10.1128\/mSystems.00030-21"},{"doi-asserted-by":"publisher","key":"R10","DOI":"10.1093\/bioinformatics\/btt086"},{"doi-asserted-by":"publisher","key":"R11","DOI":"10.1093\/bioinformatics\/btu153"},{"doi-asserted-by":"publisher","key":"R12","DOI":"10.1093\/bioinformatics\/btv271"},{"doi-asserted-by":"publisher","key":"R13","DOI":"10.1093\/nar\/gkab301"},{"doi-asserted-by":"publisher","key":"R14","DOI":"10.1007\/978-1-62703-646-7_10"},{"doi-asserted-by":"publisher","key":"R15","DOI":"10.1093\/bioinformatics\/btv421"},{"doi-asserted-by":"publisher","key":"R16","DOI":"10.1093\/molbev\/msaa015"},{"doi-asserted-by":"publisher","key":"R17","DOI":"10.1128\/AEM.02411-13"},{"doi-asserted-by":"publisher","key":"R18","DOI":"10.1093\/bioinformatics\/bti079"},{"doi-asserted-by":"publisher","key":"R19","DOI":"10.1093\/molbev\/msx335"},{"doi-asserted-by":"publisher","key":"R20","DOI":"10.1186\/s12864-015-1765-0"},{"doi-asserted-by":"publisher","key":"R21","DOI":"10.1101\/gr.1224503"},{"doi-asserted-by":"publisher","key":"R22","DOI":"10.1534\/genetics.105.048975"},{"doi-asserted-by":"publisher","key":"R23","DOI":"10.1093\/bioinformatics\/btp348"},{"doi-asserted-by":"publisher","key":"R24","DOI":"10.1038\/s41598-020-58163-8"},{"doi-asserted-by":"publisher","key":"R25","DOI":"10.1093\/bioinformatics\/btl158"},{"doi-asserted-by":"publisher","key":"R26","DOI":"10.1093\/database\/baw103"},{"doi-asserted-by":"publisher","key":"R27","DOI":"10.1016\/S0022-2836(05)80360-2"},{"doi-asserted-by":"publisher","key":"R28","DOI":"10.1101\/gr.1239303"},{"doi-asserted-by":"publisher","key":"R29","DOI":"10.1093\/bioinformatics\/btm554"},{"doi-asserted-by":"publisher","key":"R30","DOI":"10.1038\/nprot.2015.053"},{"doi-asserted-by":"publisher","key":"R31","DOI":"10.1093\/nar\/gky427"},{"doi-asserted-by":"publisher","key":"R32","DOI":"10.1002\/prot.22879"},{"doi-asserted-by":"publisher","key":"R33","DOI":"10.1016\/j.csbj.2018.01.002"},{"doi-asserted-by":"publisher","key":"R34","DOI":"10.3201\/eid2002.130118"},{"doi-asserted-by":"publisher","key":"R35","DOI":"10.1053\/j.spid.2004.09.001"},{"doi-asserted-by":"publisher","key":"R36","DOI":"10.1186\/1471-2164-15-1014"},{"doi-asserted-by":"publisher","key":"R37","DOI":"10.3390\/v14112504"},{"doi-asserted-by":"publisher","key":"R38","DOI":"10.1038\/sj.cdd.4401853"},{"doi-asserted-by":"publisher","key":"R39","DOI":"10.1073\/pnas.1215995110"},{"doi-asserted-by":"publisher","key":"R40","DOI":"10.1111\/j.1600-065X.2008.00691.x"},{"doi-asserted-by":"publisher","key":"R41","DOI":"10.1128\/JVI.06889-11"},{"doi-asserted-by":"publisher","key":"R42","DOI":"10.1128\/JVI.00304-15"},{"doi-asserted-by":"publisher","key":"R43","DOI":"10.1128\/JVI.02506-09"},{"doi-asserted-by":"publisher","key":"R44","DOI":"10.1073\/pnas.0800589105"},{"doi-asserted-by":"publisher","key":"R45","DOI":"10.1099\/vir.0.052670-0"},{"doi-asserted-by":"publisher","key":"R46","DOI":"10.1371\/journal.ppat.1010277"},{"doi-asserted-by":"publisher","key":"R47","DOI":"10.1038\/emboj.2008.143"},{"doi-asserted-by":"publisher","key":"R48","DOI":"10.1038\/nature11289"},{"doi-asserted-by":"publisher","key":"R49","DOI":"10.1038\/s41593-018-0311-1"},{"doi-asserted-by":"publisher","key":"R50","DOI":"10.1016\/j.bbapap.2006.09.006"},{"doi-asserted-by":"publisher","key":"R51","DOI":"10.1073\/pnas.0510462103"},{"doi-asserted-by":"publisher","key":"R52","DOI":"10.1186\/1756-0500-3-271"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000987?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,2]],"date-time":"2024-09-02T14:18:12Z","timestamp":1725286692000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000987"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,12]]},"references-count":52,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4,12]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000987","relation":{},"ISSN":["2057-5858"],"issn-type":[{"type":"electronic","value":"2057-5858"}],"subject":[],"published":{"date-parts":[[2023,4,12]]}}}